- "Theo convince you that he was Azrael last night, or was he acting? Someone got inside my brother's head. It's not a safe place to be."
- —Tabitha Galavan to Jim Gordon
Azrael is on the loose in Gotham City, which sparks Penguin’s need for revenge. Meanwhile, Bruce enlists the help of Selina Kyle to help track down Professor Strange, as he evades arrest for his experiments.
Jim Gordon, Harvey Bullock and several officers of the Gotham City Police Department come to Arkham Asylum with a court order to inspect the office of Hugo Strange. However, when they went into his office they found all his document shredded, which he excused as "spring cleaning". Meanwhile, Edward Nygma is returned to his cell, noticeably disturbed by the experiments he saw in Indian Hill. Because of that he decides to find a way to escape, and the opportunity presents itself in a ventilation duct installed in the ceiling of his room. Elsewhere, Azrael breaks into a church to seek a new weapon. When the priest there tells him he doesn't have any, he kills him by snapping his neck.
With Captain Barnes still recovering in the hospital, Harvey Bullock assumes the position of acting caption at the GCPD as he and Gordon have initiated a manhunt for Theo Galavan. Alvarez tells Bullock that they got six police helicopters in the air and every sniffer dog in the state looking for him. While arranging for police officers from upstate to come to Gotham to help in the manhunt, Bullock tells Tom to contact Judge Bam Bam on the phone to obtain a search warrant to search all of Arkham Asylum. Harvey then encourages the police officers present to find Galavan.
Meanwhile, Bruce has Alfred drive him into the city to meet with Selina Kyle. On the other hand, Gordon and Bullock go to Butch and Tabitha's home to talk to Tabitha Galavan about Azrael. She reveals that the sword that Azrael had used was fake, so her brother would possibly try to find the real one, which was buried with her grandfather at the Gotham Cemetery. On a rooftop, Bruce meets with Selina find a way to get into Arkham to find incriminating evidence on Hugo Strange. Initially reluctant, Selina agrees to help him after realizing the possibly that Bridgit Pike was still alive, nevertheless she decides to go alone.
Later Gordon, Bullock, and Tabitha arrive at the Gotham Cemetery to recover Azrael's actual sword, but Azrael arrives and attacks them. After savagely beating Gordon, Azrael attempts to go after him, but is enclosed in the Dumas crypt with Tabitha and she tries to reason with him to make him remember his past. Succeeding in her efforts, Theo remembers everything, including his original mission to kill Bruce Wayne. He then thanked his sister before stabbing her in the stomach as payment for her betrayal. Elsewhere in the city, Selina Kyle snuck in a laundry cart that was being put into a truck headed for Arkham.
Minutes later, Gordon was informed of what happened inside the crypt and that Theo had remembered his mission to kill Bruce Wayne. Gordon then swiftly apprehended a police car, after trying to call Wayne Manor. At Arkham Asylum, Selina Kyle was able to sneak in without being caught by climbing her way onto a building to access the air ducts. Meanwhile, Gordon drives to Wayne Manor and calls Alfred, warning him that Galavan was after Bruce once again. Right after, Bruce arrives at Wayne Manor, and Alfred informs him that Galavan was coming. In the Arkham air ducts, Selina crawls through the air ducts, where suddenly she encounters Ed who was trying to escape. Thanks to this unexpected encounter, Ed tells her how to get to Indian Hill in exchange for her telling him how to escape.
At the hospital, Butch grieves at the thought of losing Tabitha, when suddenly Penguin appears with the proposal to unite to kill Galavan for revenge for all the harm he caused to them. Meanwhile, Gordon gets a call from Alfred informing him that Bruce was home, and safe. Gordon then tells Alfred that he's coming, and turns the car around. At Wayne Manor, Bruce and Alfred split up to make sure the house was secured. While doing so, Bruce finds a broken window. In the study, Galavan confronts Alfred, and the latter refuses to take him to Bruce.
At Arkham, Selina sneaks down into the Indian Hill facility, avoiding several guards looking for Nygma on the way. At Wayne Manor, Azrael and Alfred engage each other in battle, with Bruce arriving and throwing Alfred a sword. However, Alfred is eventually defeated and thrown out of a window, with Bruce fleeing from Azrael. In the city, Gordon is held up by traffic. Down at Indian Hill, Selina overhears a conversation between Hugo Strange and Ms. Peabody in which they reveal themselves to be responsible for having sent Azrael after Jim Gordon. Hugo Strange then tells Ethel Peabody that the facility needed to be shut down, and all patients moved to a new location. When they leave, Selina sees several guards struggling to move a scaly man out his cell.
Back at Wayne Manor, Bruce runs into the car garage of the manor where he uses a car to bulldoze Azrael. Outside the manor, Azrael surprisingly stands unhurt and catches Bruce by the neck with a whip. But before he could kill Bruce with his sword, Gordon appears from behind him and shoots him with gun, though it fails to kill him. Gordon then helps Bruce to his feet and Alfred arrives, with them both tending to Bruce. Meanwhile, Azrael came to his feet, and although Gordon got out his gun to shoot him, his gun had no bullets left. However, Penguin and Butch arrive, and Butch shoots him with a rocket launcher, blowing him to smithereens. The two then leave, with Butch telling Gordon, Bruce, and Alfred good night.
At Arkham, Nygma escapes through the air duct, but the guards and their dogs instantly catch him. At the same time, Selina enters a training room where she sees a few burnt objects. There, she meets Bridgit Pike, who dressed in a new fireproof suit, prepares to burn her, thinking she was one of the test subjects sent by Professor Strange. Selina tries to reminds her they were friends and tells her about her accident, but Bridgit ignores her as she was suffering from amnesia. Failing to reason with Bridgit, Selina tries to escape the room, but suddenly all the exits are locked. Though Selina pleads with Bridgit not to attack her, Bridgit tells her that her name was Firefly before using her flamethrower. Inside the control room, Hugo Strange and Ethel Peabody watched the events unfold.